Objective To discuss rationality of the three-link model used in analysis on interactive dynamics of deep squatting, and clarify the source of differences in calculation of joint torque by three-link model and Visual 3D. Methods Eight subjects were selected to obtain kinematic data of the squat motion through Vicon. The second Lagrangian equation was used to establish the three-link dynamic equation. The joint torque was calculated based on the Mathematica programming. The results were compared with the calculation results of lower limb chain segment model by Visual 3D, and the similarity between the two results was evaluated by the coefficient of complex correlation (CMC). Results The CMC of hip joint and knee joint from 8 subjects was larger than 0.85, and the CMC of ankle joint was between 0.50-0.85. The joint torque calculated by three-link dynamic equation and Visual 3D was highly similar in hip joint and knee joint, and there was only a moderate similarity in ankle joint. Conclusions The three-link model can be used in further analysis on interactive dynamics of deep squatting, but the influence of interactive moment caused by ground reaction force (external moment) on ankle torque should be considered.